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D'Esposito D, Cappetta E, Andolfo G, Ferriello F, Borgonuovo C, Caruso G, De Natale A, Frusciante L, Ercolano MR. Deciphering the biological processes underlying tomato biomass production and composition. Plant Physiol Biochem 2019; 143:50-60. [PMID: 31479882 DOI: 10.1016/j.plaphy.2019.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/19/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
The huge amounts of biomass residues, remaining in the field after tomato fruits harvesting, can be utilized to produce bioenergy. A multiple level approach aimed to characterize two Solanum pennellii introgression lines (ILs), with contrasting phenotypes for plant architecture and biomass was carried out. The study of gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation enabled the discovery of key genes and cell processes involved biomass accumulation and composition. Enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplasts and mitochondria energy fluxes. Microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and processability.
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Affiliation(s)
- Daniela D'Esposito
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Elisa Cappetta
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Camilla Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Gianluca Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Antonino De Natale
- Department of Biology, University of Naples 'Federico II', Via Cinthia, Monte Sant'Angelo, Building 7, 80126, Naples, Italy.
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
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D’Esposito D, Ferriello F, Molin AD, Diretto G, Sacco A, Minio A, Barone A, Di Monaco R, Cavella S, Tardella L, Giuliano G, Delledonne M, Frusciante L, Ercolano MR. Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit. BMC Plant Biol 2017; 17:66. [PMID: 28347287 PMCID: PMC5369198 DOI: 10.1186/s12870-017-1008-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/27/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. We used a systems biology approach to elucidate the complex interacting mechanisms regulating the plasticity of sensorial traits. To investigate environmentally challenged transcriptomic and metabolomic remodeling and evaluate the organoleptic consequences of such variations we grown three tomato varieties, Heinz 1706, whose genome was sequenced as reference and two "local" ones, San Marzano and Vesuviano in two different locations of Campania region (Italy). RESULTS Responses to environment were more pronounced in the two "local" genotypes, rather than in the Heinz 1706. The overall genetic composition of each genotype, acting in trans, modulated the specific response to environment. Duplicated genes and transcription factors, establishing different number of network connections by gaining or losing links, play a dominant role in shaping organoleptic profile. The fundamental role of cell wall metabolism in tuning all the quality attributes, including the sensorial perception, was also highlighted. CONCLUSIONS Although similar fruit-related quality processes are activated in the same environment, different tomato genotypes follow distinct transcriptomic, metabolomic and sensorial trajectories depending on their own genetic makeup.
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Affiliation(s)
- Daniela D’Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
| | - Alessandra Dal Molin
- Department of Biotechnologies, Functional Genomics Center, University of Verona, Verona, 37134 Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Research Center, Rome, 00123 Italy
| | - Adriana Sacco
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
| | - Andrea Minio
- Department of Biotechnologies, Functional Genomics Center, University of Verona, Verona, 37134 Italy
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
| | - Rossella Di Monaco
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
| | - Silvana Cavella
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
| | - Luca Tardella
- Department of Statistical Sciences, University of Rome ‘La Sapienza’, Rome, 00185 Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Research Center, Rome, 00123 Italy
| | - Massimo Delledonne
- Department of Biotechnologies, Functional Genomics Center, University of Verona, Verona, 37134 Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Italy
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Caruso G, Gomez LD, Ferriello F, Andolfi A, Borgonuovo C, Evidente A, Simister R, McQueen-Mason SJ, Carputo D, Frusciante L, Ercolano MR. Exploring tomato Solanum pennellii introgression lines for residual biomass and enzymatic digestibility traits. BMC Genet 2016; 17:56. [PMID: 27044251 PMCID: PMC4820949 DOI: 10.1186/s12863-016-0362-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/17/2016] [Indexed: 01/09/2023] Open
Abstract
Background Residual biomass production for fuel conversion represents a unique opportunity to avoid concerns about compromising food supply by using dedicated feedstock crops. Developing tomato varieties suitable for both food consumption and fuel conversion requires the establishment of new selection methods. Results A tomato Solanum pennellii introgression population was assessed for fruit yield, biomass phenotypic diversity, and for saccharification potential. Introgression lines 2–5, 2–6, 6–3, 7–2, 10–2 and 12–4 showed the best combination of fruit and residual biomass production. Lignin, cellulose, hemicellulose content and saccharification rate showed a wide variation in the tested lines. Within hemicellulose, xylose value was high in IL 6–3, IL 7–2 and IL 6–2, whereas arabinose showed a low content in IL 10–2, IL 6–3 and IL 2–6. The latter line showed also the highest ethanol potential production. Alkali pre-treatment resulted in the highest values of saccharification in most of lines tested, suggesting that chemical pretreatment is an important factor for improving biomass processability. Interestingly, extreme genotypes for more than one single trait were found, allowing the identification of better genotypes. Cell wall related genes mapping in genomic regions involved into tomato biomass production and digestibility variation highlighted potential candidate genes. Molecular expression profile of few of them provided useful information about challenged pathways. Conclusions The screening of S. pennellii introgression population resulted very useful for delving into complex traits such as biomass production and digestibility. The extreme genotypes identified could be fruitfully employed for both genetic studies and breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0362-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- G Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - L D Gomez
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK.
| | - F Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - A Andolfi
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - C Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - A Evidente
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - R Simister
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK
| | - S J McQueen-Mason
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK
| | - D Carputo
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - L Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - M R Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy.
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Manzo D, Ferriello F, Puopolo G, Zoina A, D'Esposito D, Tardella L, Ferrarini A, Ercolano MR. Fusarium oxysporum f.sp. radicis-lycopersici induces distinct transcriptome reprogramming in resistant and susceptible isogenic tomato lines. BMC Plant Biol 2016; 16:53. [PMID: 26920134 PMCID: PMC4769521 DOI: 10.1186/s12870-016-0740-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/17/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fusarium oxysporum f.sp. radicis-lycopersici (FORL) is one of the most destructive necrotrophic pathogens affecting tomato crops, causing considerable field and greenhouse yield losses. Despite such major economic impact, little is known about the molecular mechanisms regulating Fusarium oxysporum f.sp. radicis-lycopersici resistance in tomato. RESULTS A transcriptomic experiment was carried out in order to investigate the main mechanisms of FORL response in resistant and susceptible isogenic tomato lines. Microarray analysis at 15 DPI (days post inoculum) revealed a distinct gene expression pattern between the two genotypes in the inoculated vs non-inoculated conditions. A model of plant response both for compatible and incompatible reactions was proposed. In particular, in the incompatible interaction an activation of defense genes related to secondary metabolite production and tryptophan metabolism was observed. Moreover, maintenance of the cell osmotic potential after the FORL challenging was mediated by a dehydration-induced protein. As for the compatible interaction, activation of an oxidative burst mediated by peroxidases and a cytochrome monooxygenase induced cell degeneration and necrosis. CONCLUSIONS Our work allowed comprehensive understanding of the molecular basis of the tomato-FORL interaction. The result obtained emphasizes a different transcriptional reaction between the resistant and the susceptible genotype to the FORL challenge. Our findings could lead to the improvement in disease control strategies.
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Affiliation(s)
- Daniele Manzo
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università, 100, 80055, Portici, Italy.
| | - Francesca Ferriello
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università, 100, 80055, Portici, Italy.
| | - Gerardo Puopolo
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università, 100, 80055, Portici, Italy.
- Current address: Sustainable Agro-Ecosystems and Bioresources Department - IASMA Research and Innovation Center - Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy.
| | - Astolfo Zoina
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università, 100, 80055, Portici, Italy.
| | - Daniela D'Esposito
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università, 100, 80055, Portici, Italy.
| | - Luca Tardella
- Department of Statistical Sciences, University of Rome 'La Sapienza', Rome, Italy.
| | - Alberto Ferrarini
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, Verona, Italy.
| | - Maria Raffaella Ercolano
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università, 100, 80055, Portici, Italy.
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Andolfo G, Ferriello F, Tardella L, Ferrarini A, Sigillo L, Frusciante L, Ercolano MR. Tomato genome-wide transcriptional responses to Fusarium wilt and Tomato Mosaic Virus. PLoS One 2014; 9:e94963. [PMID: 24804963 PMCID: PMC4012952 DOI: 10.1371/journal.pone.0094963] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/21/2014] [Indexed: 11/26/2022] Open
Abstract
Since gene expression approaches constitute a starting point for investigating plant–pathogen systems, we performed a transcriptional analysis to identify a set of genes of interest in tomato plants infected with F. oxysporum f. sp. lycopersici (Fol) and Tomato Mosaic Virus (ToMV). Differentially expressed tomato genes upon inoculation with Fol and ToMV were identified at two days post-inoculation. A large overlap was found in differentially expressed genes throughout the two incompatible interactions. However, Gene Ontology enrichment analysis evidenced specific categories in both interactions. Response to ToMV seems more multifaceted, since more than 70 specific categories were enriched versus the 30 detected in Fol interaction. In particular, the virus stimulated the production of an invertase enzyme that is able to redirect the flux of carbohydrates, whereas Fol induced a homeostatic response to prevent the fungus from killing cells. Genomic mapping of transcripts suggested that specific genomic regions are involved in resistance response to pathogen. Coordinated machinery could play an important role in prompting the response, since 60% of pathogen receptor genes (NB-ARC-LRR, RLP, RLK) were differentially regulated during both interactions. Assessment of genomic gene expression patterns could help in building up models of mediated resistance responses.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agriculture Sciences, University of Naples ‘Federico II’, Portici, Italy
| | - Francesca Ferriello
- Department of Agriculture Sciences, University of Naples ‘Federico II’, Portici, Italy
| | - Luca Tardella
- Department of Statistical Sciences, University of Rome ‘La Sapienza’, Rome, Italy
| | - Alberto Ferrarini
- Dipartimento di Biotecnologie - Università degli Studi di Verona, Strada le Grazie, Verona, Italy
| | - Loredana Sigillo
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - Centro di sperimentazione e certificazione delle sementi (CRA-SCS) S.S., Battipaglia (SA), Roma, Italy
| | - Luigi Frusciante
- Department of Agriculture Sciences, University of Naples ‘Federico II’, Portici, Italy
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Ercolano MR, Sacco A, Ferriello F, D'Alessandro R, Tononi P, Traini A, Barone A, Zago E, Chiusano ML, Buson G, Delledonne M, Frusciante L. Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations. BMC Genomics 2014; 15:138. [PMID: 24548308 PMCID: PMC3936818 DOI: 10.1186/1471-2164-15-138] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 01/24/2014] [Indexed: 01/08/2023] Open
Abstract
Background Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits. Results Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars. Conclusions The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.
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Affiliation(s)
- Maria Raffaella Ercolano
- Department of Agriculture Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy.
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Mazzeo MF, Cacace G, Ferriello F, Puopolo G, Zoina A, Ercolano MR, Siciliano RA. Proteomic investigation of response to FORL infection in tomato roots. Plant Physiol Biochem 2014; 74:42-9. [PMID: 24262994 DOI: 10.1016/j.plaphy.2013.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/24/2013] [Indexed: 05/07/2023]
Abstract
Fusarium oxysporum f. sp. radicis-lycopersici (FORL) leading to fusarium crown and root rot is considered one of the most destructive tomato soilborne diseases occurring in greenhouse and field crops. In this study, response to FORL infection in tomato roots was investigated by differential proteomics in susceptible (Monalbo) and resistant (Momor) isogenic tomato lines, thus leading to identify 33 proteins whose amount changed depending on the pathogen infection, and/or on the two genotypes. FORL infection induced accumulation of pathogen-related proteins (PR proteins) displaying glucanase and endochitinases activity or involved in redox processes in the Monalbo genotype. Interestingly, the level of the above mentioned PR proteins was not influenced by FORL infection in the resistant tomato line, while other proteins involved in general response mechanisms to biotic and/or abiotic stresses showed significant quantitative differences. In particular, the increased level of proteins participating to arginine metabolism and glutathione S-transferase (GST; EC 2.5.1.18) as well as that of protein LOC544002 and phosphoprotein ECPP44-like, suggested their key role in pathogen defence.
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Affiliation(s)
- Maria Fiorella Mazzeo
- Proteomic and Biomolecular Mass Spectrometry Center, Institute of Food Sciences, Italian National Research Council (CNR), Via Roma 64 a/c, 83100 Avellino, Italy
| | - Giuseppina Cacace
- Proteomic and Biomolecular Mass Spectrometry Center, Institute of Food Sciences, Italian National Research Council (CNR), Via Roma 64 a/c, 83100 Avellino, Italy
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, NA, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, TN, Italy
| | - Astolfo Zoina
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, NA, Italy
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, NA, Italy
| | - Rosa Anna Siciliano
- Proteomic and Biomolecular Mass Spectrometry Center, Institute of Food Sciences, Italian National Research Council (CNR), Via Roma 64 a/c, 83100 Avellino, Italy.
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Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L. Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects. Plant Cell Rep 2012; 31:973-85. [PMID: 22350316 PMCID: PMC3351601 DOI: 10.1007/s00299-012-1234-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/27/2012] [Accepted: 01/27/2012] [Indexed: 05/22/2023]
Abstract
Tomato (Solanum lycopersicum) is one of the world's most important vegetable crops. Managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. Tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. In this paper, we illustrate genomic methods currently employed to preserve resistant germplasm and to facilitate the study and transfer of resistance genes, and we describe the genomic organization of R-genes. Patterns of gene activation during disease resistance response, identified through functional approaches, are depicted. We also describe the opportunities offered by the use of new genomic technologies, including high-throughput DNA sequencing, large-scale expression data production and the comparative hybridization technique, whilst reporting multifaceted approaches to achieve genetic tomato disease control. Future strategies combining the huge amount of genomic and genetic data will be able to accelerate development of novel resistance varieties sustainably on a worldwide basis. Such strategies are discussed in the context of the latest insights obtained in this field.
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Affiliation(s)
- M R Ercolano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, Italy.
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